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- PDB-2zd7: The structure of VPS75 (Vacuolar protein sorting-associated prote... -

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Basic information

Entry
Database: PDB / ID: 2zd7
TitleThe structure of VPS75 (Vacuolar protein sorting-associated protein 75)
Components
  • EVDLPLSDEEPSS
  • Vacuolar protein sorting-associated protein 75
KeywordsPROTEIN TRANSPORT / Histone chaperone / vps75 / NAP1 / Nucleus / Phosphoprotein / Transport
Function / homology
Function and homology information


H3 histone acetyltransferase complex / acetyltransferase activator activity / protein modification process / double-strand break repair via nonhomologous end joining / protein transport / nucleosome assembly / histone binding / chromatin binding / chromatin / identical protein binding ...H3 histone acetyltransferase complex / acetyltransferase activator activity / protein modification process / double-strand break repair via nonhomologous end joining / protein transport / nucleosome assembly / histone binding / chromatin binding / chromatin / identical protein binding / nucleus / cytosol
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP)
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 75
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsPark, Y.J. / Luger, K.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Histone chaperone specificity in Rtt109 activation.
Authors: Park, Y.J. / Sudhoff, K.B. / Andrews, A.J. / Stargell, L.A. / Luger, K.
#1: Journal: NAT.STRUCT.MOL.BIOL. / Year: 2008
Title: Histone chaperone specificity in Rtt109 activation
Authors: Park, Y.J. / Sudhoff, K.B. / Andrews, A.J. / Stargell, L.A. / Luger, K.
History
DepositionNov 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2019Group: Database references / Source and taxonomy / Category: citation / citation_author / pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 75
B: Vacuolar protein sorting-associated protein 75
C: EVDLPLSDEEPSS


Theoretical massNumber of molelcules
Total (without water)62,7293
Polymers62,7293
Non-polymers00
Water4,792266
1
A: Vacuolar protein sorting-associated protein 75
B: Vacuolar protein sorting-associated protein 75


Theoretical massNumber of molelcules
Total (without water)61,3122
Polymers61,3122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-31 kcal/mol
Surface area24370 Å2
MethodPISA
2
C: EVDLPLSDEEPSS


Theoretical massNumber of molelcules
Total (without water)1,4161
Polymers1,4161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.692, 84.580, 86.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Vacuolar protein sorting-associated protein 75 / VPS75


Mass: 30656.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS75 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P53853
#2: Protein/peptide EVDLPLSDEEPSS


Mass: 1416.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.1 Å
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 49841 / Num. obs: 48480 / % possible obs: 95.3 % / Redundancy: 8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.4
Reflection shellResolution: 1.85→50 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 4.1 / % possible all: 93

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.85→50 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.255 9388 -
Rwork0.232 --
all-48421 -
obs-40685 95.3 %
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3725 0 0 266 3991
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.006289
X-RAY DIFFRACTIONc_angle_deg1.13951

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